Contacts of the strand formed by residues 53 - 58 (chain C) in PDB entry 1YLK
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ALA 53 (chain C).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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26C PRO* 4.0 1.1 - - - -
30C ILE* 3.6 25.8 - - + +
32C ILE* 4.3 11.9 - - + -
43C TYR* 4.1 9.0 + - - -
48C ILE* 4.0 24.0 - - + +
52C GLU* 1.3 77.8 - - - +
54C HIS* 1.3 67.0 + - - +
55C VAL* 3.8 4.6 + - + +
7D TYR* 4.0 3.4 - - + +
36D MET 4.1 0.5 - - - +
38D ALA* 3.2 24.5 + - - +
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Residues in contact with HIS 54 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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24C MET 4.7 2.0 + - - -
26C PRO* 3.5 32.1 - - + +
30C ILE 3.1 10.6 + - - +
31C ALA* 3.4 7.2 - - + -
32C ILE* 2.7 33.0 + - - +
53C ALA* 1.3 73.6 - - - +
55C VAL* 1.3 58.5 + - - +
56C ILE* 4.2 0.9 - - + -
74C SER* 2.7 31.1 + - - +
78C LEU* 3.5 27.6 - - + +
80C THR* 3.8 0.4 - - + +
504C SCN 3.1 23.3 + - - -
36D MET* 3.4 35.0 - - + +
38D ALA 3.8 9.9 + - - -
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Residues in contact with VAL 55 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
32C ILE* 3.4 20.6 - - + +
34C ALA* 5.3 0.2 - - + -
42C VAL* 4.2 24.2 - - + -
43C TYR* 3.9 25.1 - - + -
48C ILE* 4.4 4.7 - - + -
53C ALA 3.8 5.4 + - - +
54C HIS* 1.3 77.9 - - - +
56C ILE* 1.3 64.4 + - - +
57C ARG* 3.7 28.7 - - + +
36D MET* 3.2 19.7 + - - -
57D ARG* 3.2 36.6 + - - +
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Residues in contact with ILE 56 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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31C ALA* 4.7 6.3 - - + -
32C ILE 2.7 12.7 + - - +
33C VAL* 3.3 10.9 - - + -
34C ALA* 2.8 26.2 + - - +
54C HIS* 5.2 0.2 - - + -
55C VAL* 1.3 75.5 - - - +
57C ARG* 1.3 68.2 + - - +
66C ASP 5.7 0.2 - - - -
67C VAL* 3.9 28.3 - - + +
70C SER* 3.5 30.5 - - - +
71C LEU* 3.6 34.1 - - + +
74C SER* 5.4 0.2 - - - -
36D MET* 3.8 24.9 - - + -
57D ARG 3.3 12.1 - - - +
58D ASN* 4.7 1.8 - - + -
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Residues in contact with ARG 57 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C VAL* 5.5 0.2 - - - -
34C ALA* 3.2 12.8 - - + +
35C CYS 2.9 26.8 + - - +
36C MET 3.7 3.4 + - - -
37C ASP 3.1 18.6 + - - -
40C LEU* 2.7 34.9 + - - +
42C VAL* 3.7 18.0 - - - +
55C VAL* 3.7 22.4 - - + -
56C ILE* 1.3 83.9 - - - +
58C ASN* 1.3 64.7 + - - +
43D TYR* 3.9 18.6 + - - -
55D VAL* 3.2 34.1 + - - +
56D ILE* 3.4 8.4 - - - +
57D ARG* 2.8 47.1 + - + +
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Residues in contact with ASN 58 (chain C).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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33C VAL* 5.8 0.8 - - - +
34C ALA 3.3 3.4 + - - -
35C CYS* 3.3 4.2 - - - -
36C MET* 2.9 28.3 + - - -
57C ARG* 1.3 76.3 - - - +
59C ALA* 1.3 59.5 + - - +
60C GLY 3.0 7.1 + - - -
61C CYS* 3.2 4.7 + - - -
62C VAL 2.9 44.1 + - - -
64C THR* 3.8 0.4 + - - +
67C VAL* 3.3 13.1 - - - +
56D ILE* 4.6 4.7 - - + -
66D ASP* 2.7 31.3 + - - +
69D ARG* 3.4 9.4 - - - +
70D SER* 3.4 15.0 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il